HEADER VIRAL PROTEIN 16-OCT-17 5YL0 TITLE THE CRYSTAL STRUCTURE OF PENAEUS VANNAMEI NODAVIRUS P-DOMAIN (P212121) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 250-368; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PENAEUS VANNAMEI NODAVIRUS; SOURCE 3 ORGANISM_TAXID: 430911; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIRAL CAPSID PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.C.CHEN,M.YOSHIMURA,C.C.LIN,H.H.GUAN,P.CHUANKHAYAN,C.J.CHEN REVDAT 5 27-MAR-24 5YL0 1 REMARK REVDAT 4 13-MAR-19 5YL0 1 JRNL REVDAT 3 27-FEB-19 5YL0 1 JRNL REVDAT 2 07-NOV-18 5YL0 1 TITLE REVDAT 1 24-OCT-18 5YL0 0 JRNL AUTH N.C.CHEN,M.YOSHIMURA,N.MIYAZAKI,H.H.GUAN,P.CHUANKHAYAN, JRNL AUTH 2 C.C.LIN,S.K.CHEN,P.J.LIN,Y.C.HUANG,K.IWASAKI,A.NAKAGAWA, JRNL AUTH 3 S.I.CHAN,C.J.CHEN JRNL TITL THE ATOMIC STRUCTURES OF SHRIMP NODAVIRUSES REVEAL NEW JRNL TITL 2 DIMERIC SPIKE STRUCTURES AND PARTICLE POLYMORPHISM. JRNL REF COMMUN BIOL V. 2 72 2019 JRNL REFN ESSN 2399-3642 JRNL PMID 30820467 JRNL DOI 10.1038/S42003-019-0311-Z REMARK 2 REMARK 2 RESOLUTION. 1.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 3 NUMBER OF REFLECTIONS : 110940 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5861 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.22 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8284 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 428 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3321 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 1476 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.19000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : 0.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.052 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.060 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.666 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3373 ; 0.027 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3262 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4603 ; 2.137 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7540 ; 1.015 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 442 ; 7.109 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;32.349 ;26.174 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 554 ;12.023 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;19.128 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 593 ; 0.149 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3758 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 674 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1780 ; 1.312 ; 1.262 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1779 ; 1.303 ; 1.261 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2218 ; 1.777 ; 1.900 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2219 ; 1.781 ; 1.901 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1593 ; 2.574 ; 1.525 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1594 ; 2.574 ; 1.526 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2386 ; 3.819 ; 2.188 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6542 ;17.284 ;19.341 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4997 ;17.765 ;15.179 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5YL0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005467. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 134587 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.220 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.9 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 38.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 86.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43800 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.075M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1M SODIUM CACODYLATE 6.5, 30%(W/V) PEG 2000 MME, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 21.92150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.30300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.86800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.30300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.92150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.86800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 1 REMARK 465 PRO A 2 REMARK 465 THR A 3 REMARK 465 SER A 4 REMARK 465 LEU A 5 REMARK 465 THR A 6 REMARK 465 ASP A 7 REMARK 465 THR A 118 REMARK 465 SER A 119 REMARK 465 ASN B 1 REMARK 465 PRO B 2 REMARK 465 THR B 3 REMARK 465 SER B 4 REMARK 465 LEU B 5 REMARK 465 THR B 6 REMARK 465 SER B 119 REMARK 465 ASN C 1 REMARK 465 PRO C 2 REMARK 465 THR C 3 REMARK 465 SER C 4 REMARK 465 LEU C 5 REMARK 465 THR C 6 REMARK 465 SER C 119 REMARK 465 ASN D 1 REMARK 465 PRO D 2 REMARK 465 THR D 3 REMARK 465 SER D 4 REMARK 465 LEU D 5 REMARK 465 THR D 6 REMARK 465 SER D 119 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 286 O HOH B 325 1.25 REMARK 500 CB VAL A 100 O HOH A 400 1.34 REMARK 500 O HOH B 449 O HOH B 475 1.40 REMARK 500 O HOH A 529 O HOH A 531 1.41 REMARK 500 O HOH C 300 O HOH C 420 1.43 REMARK 500 CB SER C 82 O HOH C 201 1.45 REMARK 500 CE LYS A 18 O HOH A 202 1.45 REMARK 500 O HOH A 255 O HOH A 369 1.48 REMARK 500 OE1 GLU A 65 O HOH A 201 1.48 REMARK 500 O HOH C 308 O HOH C 327 1.49 REMARK 500 O HOH A 443 O HOH A 494 1.49 REMARK 500 CB THR C 91 O HOH C 224 1.49 REMARK 500 CB THR C 69 O HOH C 217 1.50 REMARK 500 O HOH D 234 O HOH D 247 1.50 REMARK 500 O HOH C 295 O HOH C 326 1.54 REMARK 500 O HOH A 372 O HOH A 406 1.54 REMARK 500 O HOH A 302 O HOH A 411 1.55 REMARK 500 O HOH B 313 O HOH B 443 1.55 REMARK 500 O HOH D 283 O HOH D 326 1.65 REMARK 500 O HOH C 237 O HOH D 371 1.66 REMARK 500 O HOH A 408 O HOH A 491 1.68 REMARK 500 O HOH D 360 O HOH D 364 1.68 REMARK 500 O HOH B 434 O HOH B 541 1.69 REMARK 500 O HOH B 222 O HOH B 461 1.70 REMARK 500 CG2 THR C 91 O HOH C 224 1.70 REMARK 500 O HOH D 204 O HOH D 405 1.70 REMARK 500 O HOH C 332 O HOH C 355 1.73 REMARK 500 CB SER B 71 O HOH B 241 1.74 REMARK 500 CD GLU B 47 O HOH B 212 1.77 REMARK 500 CB THR C 62 O HOH C 216 1.77 REMARK 500 O HOH B 346 O HOH B 401 1.78 REMARK 500 O HOH B 274 O HOH B 335 1.79 REMARK 500 SD MET C 74 O HOH C 353 1.79 REMARK 500 O HOH B 284 O HOH B 335 1.80 REMARK 500 O HOH C 355 O HOH C 406 1.80 REMARK 500 O HOH D 279 O HOH D 371 1.80 REMARK 500 O HOH D 438 O HOH D 465 1.81 REMARK 500 O HOH A 357 O HOH B 251 1.81 REMARK 500 O HOH C 235 O HOH C 457 1.82 REMARK 500 NZ LYS D 107 O HOH D 201 1.82 REMARK 500 O HOH A 374 O HOH A 397 1.83 REMARK 500 O HOH A 397 O HOH A 510 1.84 REMARK 500 CB LYS C 86 O HOH C 411 1.84 REMARK 500 O HOH A 291 O HOH A 429 1.85 REMARK 500 C ALA A 117 O HOH A 229 1.85 REMARK 500 O HOH B 227 O HOH B 229 1.85 REMARK 500 CB SER C 34 O HOH C 229 1.85 REMARK 500 O HOH A 445 O HOH A 480 1.85 REMARK 500 CG GLU B 47 O HOH B 212 1.85 REMARK 500 O HOH C 243 O HOH D 408 1.86 REMARK 500 REMARK 500 THIS ENTRY HAS 200 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH C 426 O HOH D 304 4555 1.74 REMARK 500 O HOH D 286 O HOH D 321 4455 1.77 REMARK 500 O HOH C 207 O HOH D 257 4455 1.79 REMARK 500 O HOH A 285 O HOH C 438 1655 1.84 REMARK 500 O HOH D 427 O HOH D 491 4455 1.93 REMARK 500 O HOH A 235 O HOH A 334 3744 1.96 REMARK 500 O HOH A 474 O HOH B 511 3644 1.96 REMARK 500 O HOH A 210 O HOH A 446 3744 2.03 REMARK 500 O HOH A 373 O HOH C 202 1655 2.04 REMARK 500 O HOH A 234 O HOH A 334 3744 2.06 REMARK 500 O HOH A 323 O HOH B 423 1655 2.09 REMARK 500 O HOH A 478 O HOH B 593 1655 2.13 REMARK 500 O HOH A 551 O HOH B 593 1655 2.13 REMARK 500 O HOH C 509 O HOH D 473 4455 2.17 REMARK 500 O HOH A 491 O HOH C 546 3644 2.17 REMARK 500 O HOH A 256 O HOH B 411 3744 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR B 39 CZ TYR B 39 CE2 -0.095 REMARK 500 MET B 74 SD MET B 74 CE -0.362 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 9 CD - NE - CZ ANGL. DEV. = 9.4 DEGREES REMARK 500 ARG B 9 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG B 9 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 78 77.86 -159.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 554 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A 555 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A 556 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A 557 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A 558 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A 559 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH A 560 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A 561 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH A 562 DISTANCE = 6.91 ANGSTROMS REMARK 525 HOH A 563 DISTANCE = 7.18 ANGSTROMS REMARK 525 HOH A 564 DISTANCE = 7.23 ANGSTROMS REMARK 525 HOH B 595 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH B 596 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH B 597 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH B 598 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH B 599 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH B 600 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH B 601 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH B 602 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH B 603 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH B 604 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH B 605 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH B 606 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH B 607 DISTANCE = 8.53 ANGSTROMS REMARK 525 HOH C 557 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH C 558 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH C 559 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH C 560 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH C 561 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH C 562 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH C 563 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH C 564 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH C 565 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH C 566 DISTANCE = 6.72 ANGSTROMS REMARK 525 HOH C 567 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH C 568 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH C 569 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH C 570 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH C 571 DISTANCE = 7.17 ANGSTROMS REMARK 525 HOH C 572 DISTANCE = 7.64 ANGSTROMS REMARK 525 HOH C 573 DISTANCE = 7.71 ANGSTROMS REMARK 525 HOH C 574 DISTANCE = 8.01 ANGSTROMS REMARK 525 HOH C 575 DISTANCE = 8.15 ANGSTROMS REMARK 525 HOH C 576 DISTANCE = 8.86 ANGSTROMS REMARK 525 HOH C 577 DISTANCE = 9.00 ANGSTROMS REMARK 525 HOH D 514 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH D 515 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH D 516 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH D 517 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH D 518 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH D 519 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH D 520 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH D 521 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH D 522 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH D 523 DISTANCE = 6.98 ANGSTROMS REMARK 525 HOH D 524 DISTANCE = 7.35 ANGSTROMS REMARK 525 HOH D 525 DISTANCE = 7.50 ANGSTROMS REMARK 525 HOH D 526 DISTANCE = 7.54 ANGSTROMS REMARK 525 HOH D 527 DISTANCE = 7.67 ANGSTROMS REMARK 525 HOH D 528 DISTANCE = 8.74 ANGSTROMS DBREF 5YL0 A 1 119 UNP A5H7Q8 A5H7Q8_9VIRU 250 368 DBREF 5YL0 B 1 119 UNP A5H7Q8 A5H7Q8_9VIRU 250 368 DBREF 5YL0 C 1 119 UNP A5H7Q8 A5H7Q8_9VIRU 250 368 DBREF 5YL0 D 1 119 UNP A5H7Q8 A5H7Q8_9VIRU 250 368 SEQRES 1 A 119 ASN PRO THR SER LEU THR ASP VAL ARG VAL ASP LYS ALA SEQRES 2 A 119 VAL ASN PHE ILE LYS PRO GLU VAL SER GLY VAL ALA GLU SEQRES 3 A 119 ILE GLN THR VAL THR GLY LEU SER PRO SER THR SER TYR SEQRES 4 A 119 LEU LEU THR PRO ALA PHE LEU GLU GLN ASN PHE GLN SER SEQRES 5 A 119 GLU ALA GLY ILE TYR ILE LEU SER ALA THR PRO VAL GLU SEQRES 6 A 119 GLY GLU GLY THR ILE SER ILE ASN MET ASP PRO THR VAL SEQRES 7 A 119 THR THR VAL SER GLY PHE ILE LYS VAL LYS THR ASP THR SEQRES 8 A 119 PHE GLY THR PHE ASP LEU SER VAL VAL LEU THR THR ALA SEQRES 9 A 119 SER LYS LYS GLN THR THR GLY PHE ASN ILE ILE ALA ALA SEQRES 10 A 119 THR SER SEQRES 1 B 119 ASN PRO THR SER LEU THR ASP VAL ARG VAL ASP LYS ALA SEQRES 2 B 119 VAL ASN PHE ILE LYS PRO GLU VAL SER GLY VAL ALA GLU SEQRES 3 B 119 ILE GLN THR VAL THR GLY LEU SER PRO SER THR SER TYR SEQRES 4 B 119 LEU LEU THR PRO ALA PHE LEU GLU GLN ASN PHE GLN SER SEQRES 5 B 119 GLU ALA GLY ILE TYR ILE LEU SER ALA THR PRO VAL GLU SEQRES 6 B 119 GLY GLU GLY THR ILE SER ILE ASN MET ASP PRO THR VAL SEQRES 7 B 119 THR THR VAL SER GLY PHE ILE LYS VAL LYS THR ASP THR SEQRES 8 B 119 PHE GLY THR PHE ASP LEU SER VAL VAL LEU THR THR ALA SEQRES 9 B 119 SER LYS LYS GLN THR THR GLY PHE ASN ILE ILE ALA ALA SEQRES 10 B 119 THR SER SEQRES 1 C 119 ASN PRO THR SER LEU THR ASP VAL ARG VAL ASP LYS ALA SEQRES 2 C 119 VAL ASN PHE ILE LYS PRO GLU VAL SER GLY VAL ALA GLU SEQRES 3 C 119 ILE GLN THR VAL THR GLY LEU SER PRO SER THR SER TYR SEQRES 4 C 119 LEU LEU THR PRO ALA PHE LEU GLU GLN ASN PHE GLN SER SEQRES 5 C 119 GLU ALA GLY ILE TYR ILE LEU SER ALA THR PRO VAL GLU SEQRES 6 C 119 GLY GLU GLY THR ILE SER ILE ASN MET ASP PRO THR VAL SEQRES 7 C 119 THR THR VAL SER GLY PHE ILE LYS VAL LYS THR ASP THR SEQRES 8 C 119 PHE GLY THR PHE ASP LEU SER VAL VAL LEU THR THR ALA SEQRES 9 C 119 SER LYS LYS GLN THR THR GLY PHE ASN ILE ILE ALA ALA SEQRES 10 C 119 THR SER SEQRES 1 D 119 ASN PRO THR SER LEU THR ASP VAL ARG VAL ASP LYS ALA SEQRES 2 D 119 VAL ASN PHE ILE LYS PRO GLU VAL SER GLY VAL ALA GLU SEQRES 3 D 119 ILE GLN THR VAL THR GLY LEU SER PRO SER THR SER TYR SEQRES 4 D 119 LEU LEU THR PRO ALA PHE LEU GLU GLN ASN PHE GLN SER SEQRES 5 D 119 GLU ALA GLY ILE TYR ILE LEU SER ALA THR PRO VAL GLU SEQRES 6 D 119 GLY GLU GLY THR ILE SER ILE ASN MET ASP PRO THR VAL SEQRES 7 D 119 THR THR VAL SER GLY PHE ILE LYS VAL LYS THR ASP THR SEQRES 8 D 119 PHE GLY THR PHE ASP LEU SER VAL VAL LEU THR THR ALA SEQRES 9 D 119 SER LYS LYS GLN THR THR GLY PHE ASN ILE ILE ALA ALA SEQRES 10 D 119 THR SER FORMUL 5 HOH *1476(H2 O) SHEET 1 AA1 5 ARG A 9 ASN A 15 0 SHEET 2 AA1 5 GLY A 111 ALA A 116 -1 O ILE A 114 N LYS A 12 SHEET 3 AA1 5 SER A 38 GLN A 48 -1 N LEU A 40 O ILE A 115 SHEET 4 AA1 5 ILE A 85 LYS A 88 -1 O VAL A 87 N TYR A 39 SHEET 5 AA1 5 GLU A 67 GLY A 68 -1 N GLU A 67 O LYS A 86 SHEET 1 AA2 8 ARG A 9 ASN A 15 0 SHEET 2 AA2 8 GLY A 111 ALA A 116 -1 O ILE A 114 N LYS A 12 SHEET 3 AA2 8 SER A 38 GLN A 48 -1 N LEU A 40 O ILE A 115 SHEET 4 AA2 8 THR B 79 GLY B 83 -1 O THR B 79 N GLN A 48 SHEET 5 AA2 8 ILE B 70 ASN B 73 -1 N ASN B 73 O THR B 80 SHEET 6 AA2 8 ILE B 58 PRO B 63 -1 N ALA B 61 O ILE B 70 SHEET 7 AA2 8 PHE B 95 LEU B 101 -1 O SER B 98 N THR B 62 SHEET 8 AA2 8 GLU B 26 VAL B 30 -1 N GLU B 26 O VAL B 99 SHEET 1 AA3 8 GLU A 26 VAL A 30 0 SHEET 2 AA3 8 PHE A 95 LEU A 101 -1 O PHE A 95 N VAL A 30 SHEET 3 AA3 8 ILE A 58 PRO A 63 -1 N THR A 62 O SER A 98 SHEET 4 AA3 8 ILE A 70 ASN A 73 -1 O ILE A 72 N LEU A 59 SHEET 5 AA3 8 THR A 79 SER A 82 -1 O THR A 80 N ASN A 73 SHEET 6 AA3 8 SER B 38 GLN B 48 -1 O GLN B 48 N THR A 79 SHEET 7 AA3 8 GLY B 111 ALA B 117 -1 O ILE B 115 N LEU B 40 SHEET 8 AA3 8 VAL B 8 ASN B 15 -1 N ARG B 9 O ALA B 116 SHEET 1 AA4 7 GLU A 26 VAL A 30 0 SHEET 2 AA4 7 PHE A 95 LEU A 101 -1 O PHE A 95 N VAL A 30 SHEET 3 AA4 7 ILE A 58 PRO A 63 -1 N THR A 62 O SER A 98 SHEET 4 AA4 7 ILE A 70 ASN A 73 -1 O ILE A 72 N LEU A 59 SHEET 5 AA4 7 THR A 79 SER A 82 -1 O THR A 80 N ASN A 73 SHEET 6 AA4 7 SER B 38 GLN B 48 -1 O GLN B 48 N THR A 79 SHEET 7 AA4 7 ILE B 85 LYS B 88 -1 O ILE B 85 N LEU B 41 SHEET 1 AA5 5 VAL C 8 ASN C 15 0 SHEET 2 AA5 5 GLY C 111 ALA C 117 -1 O ILE C 114 N ASP C 11 SHEET 3 AA5 5 SER C 38 GLN C 48 -1 N LEU C 40 O ILE C 115 SHEET 4 AA5 5 ILE C 85 LYS C 88 -1 O VAL C 87 N TYR C 39 SHEET 5 AA5 5 GLY C 66 GLY C 68 -1 N GLU C 67 O LYS C 86 SHEET 1 AA611 GLU C 26 VAL C 30 0 SHEET 2 AA611 PHE C 95 LEU C 101 -1 O LEU C 97 N GLN C 28 SHEET 3 AA611 ILE C 58 PRO C 63 -1 N THR C 62 O SER C 98 SHEET 4 AA611 ILE C 70 ASN C 73 -1 O ILE C 72 N LEU C 59 SHEET 5 AA611 THR C 79 SER C 82 -1 O THR C 80 N ASN C 73 SHEET 6 AA611 SER D 38 GLN D 48 -1 O GLN D 48 N THR C 79 SHEET 7 AA611 THR D 79 LYS D 88 -1 O ILE D 85 N LEU D 41 SHEET 8 AA611 GLY D 66 ASN D 73 -1 N ASN D 73 O THR D 80 SHEET 9 AA611 ILE D 58 PRO D 63 -1 N LEU D 59 O ILE D 72 SHEET 10 AA611 PHE D 95 LEU D 101 -1 O SER D 98 N THR D 62 SHEET 11 AA611 GLU D 26 VAL D 30 -1 N GLN D 28 O LEU D 97 SHEET 1 AA7 7 VAL D 8 ASN D 15 0 SHEET 2 AA7 7 GLY D 111 ALA D 117 -1 O ILE D 114 N LYS D 12 SHEET 3 AA7 7 SER D 38 GLN D 48 -1 N LEU D 40 O ILE D 115 SHEET 4 AA7 7 THR D 79 LYS D 88 -1 O ILE D 85 N LEU D 41 SHEET 5 AA7 7 SER C 38 GLN C 48 -1 N GLN C 48 O THR D 79 SHEET 6 AA7 7 ILE C 85 LYS C 88 -1 O VAL C 87 N TYR C 39 SHEET 7 AA7 7 GLY C 66 GLY C 68 -1 N GLU C 67 O LYS C 86 CRYST1 43.843 69.736 146.606 90.00 90.00 90.00 P 21 21 21 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.022809 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014340 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006821 0.00000